| Variant ID: vg0319757112 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 19757112 |
| Reference Allele: C | Alternative Allele: CT |
| Primary Allele: C | Secondary Allele: CT |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 300. )
TCGCTAATGAGGCAAGAACCATGGTTGTTGGTGGTATCATCATCATTAGTATTGCTAGTGTTGTTGTCTGCATTGCGTCCATCTTCTTGGGGCAGGAACT[C/CT]
TTGATGCACAACAGAAGATCCGGTGATCTGAAGTGGCTCAGTGCGCTGTCTTTGGTTACCACATGGAAATACTGGGATGTTGACAATCCTCCTCTTGCAG
CTGCAAGAGGAGGATTGTCAACATCCCAGTATTTCCATGTGGTAACCAAAGACAGCGCACTGAGCCACTTCAGATCACCGGATCTTCTGTTGTGCATCAA[G/AG]
AGTTCCTGCCCCAAGAAGATGGACGCAATGCAGACAACAACACTAGCAATACTAATGATGATGATACCACCAACAACCATGGTTCTTGCCTCATTAGCGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.50% | 0.40% | 3.66% | 62.36% | NA |
| All Indica | 2759 | 6.00% | 0.80% | 4.28% | 88.98% | NA |
| All Japonica | 1512 | 83.40% | 0.00% | 3.17% | 13.43% | NA |
| Aus | 269 | 13.00% | 0.00% | 0.74% | 86.25% | NA |
| Indica I | 595 | 4.40% | 0.00% | 2.18% | 93.45% | NA |
| Indica II | 465 | 4.90% | 0.90% | 3.66% | 90.54% | NA |
| Indica III | 913 | 5.90% | 1.50% | 6.68% | 85.87% | NA |
| Indica Intermediate | 786 | 7.90% | 0.40% | 3.44% | 88.30% | NA |
| Temperate Japonica | 767 | 94.40% | 0.00% | 0.91% | 4.69% | NA |
| Tropical Japonica | 504 | 65.70% | 0.00% | 5.95% | 28.37% | NA |
| Japonica Intermediate | 241 | 85.50% | 0.00% | 4.56% | 9.96% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 5.56% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0319757112 | C -> DEL | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0319757112 | C -> CT | LOC_Os03g35670.1 | N | frameshift_variant | Average:4.371; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |